9CBQ | pdb_00009cbq

Methionine synthase from Thermus thermophilus HB8, Folate demethylation state (Fol-on)

• PDB DOI: https://doi.org/10.2210/pdb9CBQ/pdb

• Classification: TRANSFERASE
• Organism(s): Thermus thermophilus HB8
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2024-06-19 Released: 2025-07-02 
• Deposition Author(s): Yamada, K., Mendoza, J., Koutmos, M.
• Funding Organization(s): National Science Foundation (NSF, United States)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.87 Å
• R-Value Free: 
  0.273 (Depositor) 
• R-Value Work: 
  0.210 (Depositor) 
• R-Value Observed: 
  0.213 (Depositor) 

Starting Model: experimental

Literature

Methionine synthase from Thermus thermophilus HB8, Folate demethylation state (Fol-on)

Mendoza, J., Yamada, K., Koutmos, M.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 58.6 kDa 
• Atom Count: 4,020 
• Modeled Residue Count: 496 
• Deposited Residue Count: 511 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methionine synthase	A	511	Thermus thermophilus HB8	Mutation(s): 1  Gene Names: TTHA0618 EC: 2.1.1.13
UniProt
Find proteins for Q5SKM5 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SKM5  Go to UniProtKB:  Q5SKM5

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
B12 (Subject of Investigation/LOI)	B [auth A]	COBALAMIN C62 H89 Co N13 O14 P LKVIQTCSMMVGFU-DWSMJLPVSA-N
NHE	D [auth A]	2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID C8 H17 N O3 S MKWKNSIESPFAQN-UHFFFAOYSA-N
SO4	C [auth A], G [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
BUA (Subject of Investigation/LOI)	H [auth A]	butanoic acid C4 H8 O2 FERIUCNNQQJTOY-UHFFFAOYSA-N
ZN	F [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.87 Å
• R-Value Free:  0.273 (Depositor) 
• R-Value Work:  0.210 (Depositor) 
• R-Value Observed: 0.213 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 95.164	α = 90
b = 95.164	β = 90
c = 274.337	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
DIALS	data reduction
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-07-02 
Deposition Author(s): Yamada, K., Mendoza, J., Koutmos, M.

---

Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	1945174

Revision History  

• Version 1.0: 2025-07-02
  Type: Initial release
  
• Version 2.0: 2025-09-03
  Type: Coordinate replacement
  Reason: Model completeness
  Changes: Atomic model, Author supporting evidence, Data collection, Database references, Derived calculations, Non-polymer description, Refinement description, Structure summary